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Series GSE128430 Query DataSets for GSE128430
Status Public on Jul 16, 2019
Title ChIP-seq and RNA-seq analyses of genomic regulators in Pseudomonas aeruginosa
Organism Pseudomonas aeruginosa PAO1
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Regulatory networks including virulence-related transcriptional factors (TFs) determine bacterial pathogenicity in response to different environmental cues. Pseudomonas aeruginosa, a Gram-negative opportunistic pathogen of humans, recruits numerous TFs in quorum sensing (QS) system, type III secretion system (T3SS) and Type VI secretion system (T6SS) to mediate the pathogenicity. Although many virulence-related TFs have been illustrated individually, very little is known about their crosstalks and regulatory network. Here, based on chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and transcriptome profiling (RNA-seq), we primarily focused on understanding the crosstalks of 20 virulence-related TFs, which led to construction of a virulence regulatory network named PAGnet (Pseudomonas aeruginosa Genomic integrated regulatory network), including 82 crosstalk targets. The PAGnet uncovered the intricate mechanism of virulence regulation and revealed master regulators in QS, T3SS and T6SS pathways. In particular, GacA and ExsA showed novel functions in QS and nitrogen metabolism. In addition, an online PAGnet platform was provided to analyze these TFs and more virulence factors. Taken together, the present study revealed the function-specific crosstalks of virulence regulatory network, which might provide new strategies for treating infections in P. aeruginosa in the future.
 
Overall design ChIP-seq and RNA-seq analyses of genomic regulators in Pseudomonas aeruginosa
Please note that the processed data generated from both replicates is linked to the corresponding rep1 sample records.
 
Contributor(s) Deng X
Citation(s) 31270321
Submission date Mar 18, 2019
Last update date Jul 16, 2019
Contact name Xin DENG
E-mail(s) xindeng@cityu.edu.hk
Phone 852-34425693
Organization name City University of Hong Kong
Department Department of Biomedical Sciences
Lab Dr Xin DENG's Lab
Street address 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong
City Hong Kong
ZIP/Postal code 000000
Country Hong Kong
 
Platforms (1)
GPL19430 Illumina HiSeq 2000 (Pseudomonas aeruginosa PAO1)
Samples (52)
GSM3674388 FleQ1
GSM3674389 FleQ2
GSM3674390 GbdR1
Relations
BioProject PRJNA527727
SRA SRP188684

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE128430_QscR_RNA-seq_analyzed.xlsx 410.0 Kb (ftp)(http) XLSX
GSE128430_RAW.tar 5.7 Mb (http)(custom) TAR (of TXT, XLSX)
GSE128430_VqsM_RNA-seq_analyzed.xlsx 447.5 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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